MolNFT v1 · #188336 · protein
V-ATPase from saccharomyces cerevisiae, state 1
7TMR · H(+)-transporting two-sector ATPase: “V-ATPase from saccharomyces cerevisiae, state 1”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.90). MolNFT v1 #188336 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7TMR
- Type
- protein
- Length
- 8,224 residues
- Chains
- 31
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H(+)-transporting two-sector ATPase; Vacuolar proton pump subunit B; V-type proton ATPase…
- EC
- 7.1.2.2
- UniProt
- B3LH69, A0A6A5Q585, A0A6A5Q7Y8, P48836, A0A6A5Q1W2, A0A6A5PYF6, A0A6A5PTP1, P41807, P32563, P53262, P23968, P32366, Q3E7B6, P0C5R9, P25515, P32842
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 22 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | H(+)-transporting two-sector ATPase (EC 7.1.2.2) | protein | 593 | 37% helix, 22% strand | B3LH69 |
| B | Vacuolar proton pump subunit B | protein | 475 | 37% helix, 21% strand | A0A6A5Q585 |
| D | Vacuolar proton pump subunit B | protein | 475 | 34% helix, 25% strand | A0A6A5Q585 |
| F | Vacuolar proton pump subunit B | protein | 478 | 35% helix, 23% strand | A0A6A5Q585 |
| G | V-type proton ATPase subunit E | protein | 221 | 67% helix, 8% strand | A0A6A5Q7Y8 |
| H | V-type proton ATPase subunit G | protein | 112 | 87% helix, 0% strand | P48836 |
| I | V-type proton ATPase subunit E | protein | 221 | 71% helix, 9% strand | A0A6A5Q7Y8 |
| J, L | V-type proton ATPase subunit G | protein | 111 | 91% helix, 0% strand | P48836 |
| K | V-type proton ATPase subunit E | protein | 225 | 71% helix, 8% strand | A0A6A5Q7Y8 |
| M | V-type proton ATPase subunit D | protein | 214 | 74% helix, 7% strand | A0A6A5Q1W2 |
| N | V-type proton ATPase subunit F | protein | 115 | 39% helix, 17% strand | A0A6A5PYF6 |
| O | V-type proton ATPase subunit C | protein | 364 | 48% helix, 7% strand | A0A6A5PTP1 |
| P | V-type proton ATPase subunit H | protein | 441 | 77% helix, 0% strand | P41807 |
| a | V-type proton ATPase subunit a, vacuolar isoform | protein | 734 | 60% helix, 6% strand | P32563 |
| b | V0 assembly protein 1 | protein | 52 | 52% helix, 0% strand | P53262 |
| c | V-type proton ATPase subunit C'' | protein | 198 | 86% helix, 0% strand | P23968 |
| d | V-type proton ATPase subunit D | protein | 343 | 69% helix, 0% strand | P32366 |
| e | V-type proton ATPase subunit E | protein | 64 | 72% helix, 2% strand | Q3E7B6 |
| f | Yeast V-ATPase subunit F | protein | 63 | 70% helix, 0% strand | P0C5R9 |
| g, h, i, k, l, m, n | V-type proton ATPase subunit C | protein | 159 | 77% helix, 0% strand | P25515 |
| j | V-type proton ATPase subunit C | protein | 157 | 82% helix, 0% strand | P25515 |
| o | V-type proton ATPase subunit C' | protein | 158 | 82% helix, 0% strand | P32842 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.90 | 0.94 | 147 | ADP |
| 2 | 803 | 0.87 | 0.89 | 100 | empty |
| 3 | 643 | 0.85 | 0.89 | 107 | empty |
| 4 | 687 | 0.84 | 0.89 | 79 | empty |
| 5 | 1082 | 0.83 | 0.84 | 103 | empty |
Interfaces
69 interfaces between chains.
- E–F · 2943 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2446 Ų buried · 26 hydrogen bonds · protein-protein
- D–K · 2094 Ų buried · 21 hydrogen bonds · protein-protein
- a–e · 2078 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1900 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7TMR · V-ATPase from Saccharomyces cerevisiae, State 1 · the same entry in another collection · chain J against J, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B3LH69
- Every structure of UniProt A0A6A5Q585
- Every structure of UniProt A0A6A5Q7Y8
- Every structure of UniProt P48836
- Every structure of UniProt A0A6A5Q1W2
- Every structure of UniProt A0A6A5PYF6
- Every structure of UniProt A0A6A5PTP1
- Every structure of UniProt P41807
- Every structure of UniProt P32563
- Every structure of UniProt P53262
- Every structure of UniProt P23968
- Every structure of UniProt P32366
- Every structure of UniProt Q3E7B6
- Every structure of UniProt P0C5R9
- Every structure of UniProt P25515
- Every structure of UniProt P32842
- Elsewhere: RCSB PDB 7TMR · PDBe 7TMR · UniProt B3LH69 · UniProt A0A6A5Q585 · UniProt A0A6A5Q7Y8 · UniProt P48836 · UniProt A0A6A5Q1W2 · UniProt A0A6A5PYF6 · UniProt A0A6A5PTP1 · UniProt P41807 · UniProt P32563 · UniProt P53262 · UniProt P23968 · UniProt P32366 · UniProt Q3E7B6 · UniProt P0C5R9 · UniProt P25515 · UniProt P32842
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